When reading a pdf, there are little points that you have to mention in addition. An ability to have a small window/ note beside the main pdf to mention them would be amazing. every time you go over that page, it would tell you that there you have x number of notes on this, or better, it would highlight those lines so you know that there is additional info with those

The other thing that could be added is the ability to connect boxes to each other like in liquid text